2. Input data for analysis

4. Users that have expression values (dataset 1_ chicken affy_foldchane.txt. can upload that file as shown in slide 30

5. Input data format More information available in IPA_workshop.doc

6. Save input data as a new project including metadata

7. Create analysis

8. Analysis settings Applying filters Information about mapped/unmapped data More information available in IPA_workshop.doc

9. Unmapped IDs

10. Mapped Ids

11. Run Analysis

12. Progress of analysis

13. Analysis summary Export

14. Networks tab of analysis

15. Select and view network Right click

16. Top network

17. Functions tab Biological functions More information available in IPA_workshop.doc

18. Customize functions

19. Molecular and cellular functions only Export options

20. Export functions

21. Navigate the functions displayed as a DAG

22. Canonical pathways

23. Customize pathways Statistical scoring

24. Signaling pathways

25. Coverage i.e. ratio Of pathways

26. Entities in the pathway

27. TREM1 signaling pathway

29. Data input with fold change

31. Networks tab. Genes have associated fold change (decrease (green) and increase (red))

32. Top network with fold change

33. TREM1 signaling Some IPA results are available in the folder entitled IPA_results

34. TREM1 signaling

35. Search analysis results

36. Results of search for ‘invasion’

37. Creating lists from Functions tab

38. Select a set of genes and save as ‘new list’

40. Selected lists can be exported to additional tools

41. List exported as a ‘new pathway’

42. Connect all entities in the list Select all entities

43. Build connections

44. Build connections applying all desired filters More information available in IPA_workshop.doc

45. Interconnected genes from the list Save as a new pathway

46. Saved list & pathway

47. Overlay expression values to the new pathway

48. Select analyzed dataset

49. Acknowledgement Ingenuity Pathways Analysis (web and help manual) IPA offers weekly (Thursday) training http://www.ingenuity.com/products/training.html Additional IPA resources http://www.ingenuity.com/library/index.html